Freud's idea of the superego is that it develops in the first five years or so of a person's life as a response to how he is parented; the child internalizes the parents' and greater society's moral standards.
A consistent example of the superego throughout Lord of the Flies is Piggy. He often offers a "parental" voice, and his glasses and substantial physique suggest he is older and wiser than the boys. An example of this appears in chapter 3 when he wears "the martyred expression of a parent who has to keep up with the senseless ebullience of the children" and reclaims the conch, the symbol of order and civility, from Ralph.
Golding also indirectly references the superego in chapter 4 when Maurice and Roger destroy the sandcastles the littluns have built on the beach then bury the flowers and stones the children are playing with. Roger shows no shame, but Maurice hurries away from the scene. The narrator observes:
In his other life Maurice had received chastisement for filling a younger eye with sand. Now, though there was no parent to let fall a heavy hand, Maurice still felt the unease of wrongdoing.
Maurice's discomfort with the harm done to the littluns suggests his superego has been triggered.
(Page numbers will vary because of the many available editions of the novel.)